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import numpy as np
import pytest
from numpy.testing import assert_allclose
from scipy.stats.mstats import mquantiles
from sklearn.compose import make_column_transformer
from sklearn.datasets import (
load_diabetes,
load_iris,
make_classification,
make_regression,
)
from sklearn.ensemble import GradientBoostingClassifier, GradientBoostingRegressor
from sklearn.inspection import PartialDependenceDisplay
from sklearn.linear_model import LinearRegression
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import OneHotEncoder
from sklearn.utils._testing import _convert_container
# TODO: Remove when https://github.com/numpy/numpy/issues/14397 is resolved
pytestmark = pytest.mark.filterwarnings(
(
"ignore:In future, it will be an error for 'np.bool_':DeprecationWarning:"
"matplotlib.*"
),
)
@pytest.fixture(scope="module")
def diabetes():
# diabetes dataset, subsampled for speed
data = load_diabetes()
data.data = data.data[:50]
data.target = data.target[:50]
return data
@pytest.fixture(scope="module")
def clf_diabetes(diabetes):
clf = GradientBoostingRegressor(n_estimators=10, random_state=1)
clf.fit(diabetes.data, diabetes.target)
return clf
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize("grid_resolution", [10, 20])
def test_plot_partial_dependence(grid_resolution, pyplot, clf_diabetes, diabetes):
# Test partial dependence plot function.
# Use columns 0 & 2 as 1 is not quantitative (sex)
feature_names = diabetes.feature_names
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 2, (0, 2)],
grid_resolution=grid_resolution,
feature_names=feature_names,
contour_kw={"cmap": "jet"},
)
fig = pyplot.gcf()
axs = fig.get_axes()
assert disp.figure_ is fig
assert len(axs) == 4
assert disp.bounding_ax_ is not None
assert disp.axes_.shape == (1, 3)
assert disp.lines_.shape == (1, 3)
assert disp.contours_.shape == (1, 3)
assert disp.deciles_vlines_.shape == (1, 3)
assert disp.deciles_hlines_.shape == (1, 3)
assert disp.lines_[0, 2] is None
assert disp.contours_[0, 0] is None
assert disp.contours_[0, 1] is None
# deciles lines: always show on xaxis, only show on yaxis if 2-way PDP
for i in range(3):
assert disp.deciles_vlines_[0, i] is not None
assert disp.deciles_hlines_[0, 0] is None
assert disp.deciles_hlines_[0, 1] is None
assert disp.deciles_hlines_[0, 2] is not None
assert disp.features == [(0,), (2,), (0, 2)]
assert np.all(disp.feature_names == feature_names)
assert len(disp.deciles) == 2
for i in [0, 2]:
assert_allclose(
disp.deciles[i],
mquantiles(diabetes.data[:, i], prob=np.arange(0.1, 1.0, 0.1)),
)
single_feature_positions = [(0, (0, 0)), (2, (0, 1))]
expected_ylabels = ["Partial dependence", ""]
for i, (feat_col, pos) in enumerate(single_feature_positions):
ax = disp.axes_[pos]
assert ax.get_ylabel() == expected_ylabels[i]
assert ax.get_xlabel() == diabetes.feature_names[feat_col]
line = disp.lines_[pos]
avg_preds = disp.pd_results[i]
assert avg_preds.average.shape == (1, grid_resolution)
target_idx = disp.target_idx
line_data = line.get_data()
assert_allclose(line_data[0], avg_preds["grid_values"][0])
assert_allclose(line_data[1], avg_preds.average[target_idx].ravel())
# two feature position
ax = disp.axes_[0, 2]
coutour = disp.contours_[0, 2]
assert coutour.get_cmap().name == "jet"
assert ax.get_xlabel() == diabetes.feature_names[0]
assert ax.get_ylabel() == diabetes.feature_names[2]
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize(
"kind, centered, subsample, shape",
[
("average", False, None, (1, 3)),
("individual", False, None, (1, 3, 50)),
("both", False, None, (1, 3, 51)),
("individual", False, 20, (1, 3, 20)),
("both", False, 20, (1, 3, 21)),
("individual", False, 0.5, (1, 3, 25)),
("both", False, 0.5, (1, 3, 26)),
("average", True, None, (1, 3)),
("individual", True, None, (1, 3, 50)),
("both", True, None, (1, 3, 51)),
("individual", True, 20, (1, 3, 20)),
("both", True, 20, (1, 3, 21)),
],
)
def test_plot_partial_dependence_kind(
pyplot,
kind,
centered,
subsample,
shape,
clf_diabetes,
diabetes,
):
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 1, 2],
kind=kind,
centered=centered,
subsample=subsample,
)
assert disp.axes_.shape == (1, 3)
assert disp.lines_.shape == shape
assert disp.contours_.shape == (1, 3)
assert disp.contours_[0, 0] is None
assert disp.contours_[0, 1] is None
assert disp.contours_[0, 2] is None
if centered:
assert all([ln._y[0] == 0.0 for ln in disp.lines_.ravel() if ln is not None])
else:
assert all([ln._y[0] != 0.0 for ln in disp.lines_.ravel() if ln is not None])
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize(
"input_type, feature_names_type",
[
("dataframe", None),
("dataframe", "list"),
("list", "list"),
("array", "list"),
("dataframe", "array"),
("list", "array"),
("array", "array"),
("dataframe", "series"),
("list", "series"),
("array", "series"),
("dataframe", "index"),
("list", "index"),
("array", "index"),
],
)
def test_plot_partial_dependence_str_features(
pyplot,
clf_diabetes,
diabetes,
input_type,
feature_names_type,
):
if input_type == "dataframe":
pd = pytest.importorskip("pandas")
X = pd.DataFrame(diabetes.data, columns=diabetes.feature_names)
elif input_type == "list":
X = diabetes.data.tolist()
else:
X = diabetes.data
if feature_names_type is None:
feature_names = None
else:
feature_names = _convert_container(diabetes.feature_names, feature_names_type)
grid_resolution = 25
# check with str features and array feature names and single column
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
X,
[("age", "bmi"), "bmi"],
grid_resolution=grid_resolution,
feature_names=feature_names,
n_cols=1,
line_kw={"alpha": 0.8},
)
fig = pyplot.gcf()
axs = fig.get_axes()
assert len(axs) == 3
assert disp.figure_ is fig
assert disp.axes_.shape == (2, 1)
assert disp.lines_.shape == (2, 1)
assert disp.contours_.shape == (2, 1)
assert disp.deciles_vlines_.shape == (2, 1)
assert disp.deciles_hlines_.shape == (2, 1)
assert disp.lines_[0, 0] is None
assert disp.deciles_vlines_[0, 0] is not None
assert disp.deciles_hlines_[0, 0] is not None
assert disp.contours_[1, 0] is None
assert disp.deciles_hlines_[1, 0] is None
assert disp.deciles_vlines_[1, 0] is not None
# line
ax = disp.axes_[1, 0]
assert ax.get_xlabel() == "bmi"
assert ax.get_ylabel() == "Partial dependence"
line = disp.lines_[1, 0]
avg_preds = disp.pd_results[1]
target_idx = disp.target_idx
assert line.get_alpha() == 0.8
line_data = line.get_data()
assert_allclose(line_data[0], avg_preds["grid_values"][0])
assert_allclose(line_data[1], avg_preds.average[target_idx].ravel())
# contour
ax = disp.axes_[0, 0]
assert ax.get_xlabel() == "age"
assert ax.get_ylabel() == "bmi"
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
def test_plot_partial_dependence_custom_axes(pyplot, clf_diabetes, diabetes):
grid_resolution = 25
fig, (ax1, ax2) = pyplot.subplots(1, 2)
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
["age", ("age", "bmi")],
grid_resolution=grid_resolution,
feature_names=diabetes.feature_names,
ax=[ax1, ax2],
)
assert fig is disp.figure_
assert disp.bounding_ax_ is None
assert disp.axes_.shape == (2,)
assert disp.axes_[0] is ax1
assert disp.axes_[1] is ax2
ax = disp.axes_[0]
assert ax.get_xlabel() == "age"
assert ax.get_ylabel() == "Partial dependence"
line = disp.lines_[0]
avg_preds = disp.pd_results[0]
target_idx = disp.target_idx
line_data = line.get_data()
assert_allclose(line_data[0], avg_preds["grid_values"][0])
assert_allclose(line_data[1], avg_preds.average[target_idx].ravel())
# contour
ax = disp.axes_[1]
assert ax.get_xlabel() == "age"
assert ax.get_ylabel() == "bmi"
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize(
"kind, lines", [("average", 1), ("individual", 50), ("both", 51)]
)
def test_plot_partial_dependence_passing_numpy_axes(
pyplot, clf_diabetes, diabetes, kind, lines
):
grid_resolution = 25
feature_names = diabetes.feature_names
disp1 = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
["age", "bmi"],
kind=kind,
grid_resolution=grid_resolution,
feature_names=feature_names,
)
assert disp1.axes_.shape == (1, 2)
assert disp1.axes_[0, 0].get_ylabel() == "Partial dependence"
assert disp1.axes_[0, 1].get_ylabel() == ""
assert len(disp1.axes_[0, 0].get_lines()) == lines
assert len(disp1.axes_[0, 1].get_lines()) == lines
lr = LinearRegression()
lr.fit(diabetes.data, diabetes.target)
disp2 = PartialDependenceDisplay.from_estimator(
lr,
diabetes.data,
["age", "bmi"],
kind=kind,
grid_resolution=grid_resolution,
feature_names=feature_names,
ax=disp1.axes_,
)
assert np.all(disp1.axes_ == disp2.axes_)
assert len(disp2.axes_[0, 0].get_lines()) == 2 * lines
assert len(disp2.axes_[0, 1].get_lines()) == 2 * lines
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize("nrows, ncols", [(2, 2), (3, 1)])
def test_plot_partial_dependence_incorrent_num_axes(
pyplot, clf_diabetes, diabetes, nrows, ncols
):
grid_resolution = 5
fig, axes = pyplot.subplots(nrows, ncols)
axes_formats = [list(axes.ravel()), tuple(axes.ravel()), axes]
msg = "Expected ax to have 2 axes, got {}".format(nrows * ncols)
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
["age", "bmi"],
grid_resolution=grid_resolution,
feature_names=diabetes.feature_names,
)
for ax_format in axes_formats:
with pytest.raises(ValueError, match=msg):
PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
["age", "bmi"],
grid_resolution=grid_resolution,
feature_names=diabetes.feature_names,
ax=ax_format,
)
# with axes object
with pytest.raises(ValueError, match=msg):
disp.plot(ax=ax_format)
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
def test_plot_partial_dependence_with_same_axes(pyplot, clf_diabetes, diabetes):
# The first call to plot_partial_dependence will create two new axes to
# place in the space of the passed in axes, which results in a total of
# three axes in the figure.
# Currently the API does not allow for the second call to
# plot_partial_dependence to use the same axes again, because it will
# create two new axes in the space resulting in five axes. To get the
# expected behavior one needs to pass the generated axes into the second
# call:
# disp1 = plot_partial_dependence(...)
# disp2 = plot_partial_dependence(..., ax=disp1.axes_)
grid_resolution = 25
fig, ax = pyplot.subplots()
PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
["age", "bmi"],
grid_resolution=grid_resolution,
feature_names=diabetes.feature_names,
ax=ax,
)
msg = (
"The ax was already used in another plot function, please set "
"ax=display.axes_ instead"
)
with pytest.raises(ValueError, match=msg):
PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
["age", "bmi"],
grid_resolution=grid_resolution,
feature_names=diabetes.feature_names,
ax=ax,
)
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
def test_plot_partial_dependence_feature_name_reuse(pyplot, clf_diabetes, diabetes):
# second call to plot does not change the feature names from the first
# call
feature_names = diabetes.feature_names
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 1],
grid_resolution=10,
feature_names=feature_names,
)
PartialDependenceDisplay.from_estimator(
clf_diabetes, diabetes.data, [0, 1], grid_resolution=10, ax=disp.axes_
)
for i, ax in enumerate(disp.axes_.ravel()):
assert ax.get_xlabel() == feature_names[i]
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
def test_plot_partial_dependence_multiclass(pyplot):
grid_resolution = 25
clf_int = GradientBoostingClassifier(n_estimators=10, random_state=1)
iris = load_iris()
# Test partial dependence plot function on multi-class input.
clf_int.fit(iris.data, iris.target)
disp_target_0 = PartialDependenceDisplay.from_estimator(
clf_int, iris.data, [0, 3], target=0, grid_resolution=grid_resolution
)
assert disp_target_0.figure_ is pyplot.gcf()
assert disp_target_0.axes_.shape == (1, 2)
assert disp_target_0.lines_.shape == (1, 2)
assert disp_target_0.contours_.shape == (1, 2)
assert disp_target_0.deciles_vlines_.shape == (1, 2)
assert disp_target_0.deciles_hlines_.shape == (1, 2)
assert all(c is None for c in disp_target_0.contours_.flat)
assert disp_target_0.target_idx == 0
# now with symbol labels
target = iris.target_names[iris.target]
clf_symbol = GradientBoostingClassifier(n_estimators=10, random_state=1)
clf_symbol.fit(iris.data, target)
disp_symbol = PartialDependenceDisplay.from_estimator(
clf_symbol, iris.data, [0, 3], target="setosa", grid_resolution=grid_resolution
)
assert disp_symbol.figure_ is pyplot.gcf()
assert disp_symbol.axes_.shape == (1, 2)
assert disp_symbol.lines_.shape == (1, 2)
assert disp_symbol.contours_.shape == (1, 2)
assert disp_symbol.deciles_vlines_.shape == (1, 2)
assert disp_symbol.deciles_hlines_.shape == (1, 2)
assert all(c is None for c in disp_symbol.contours_.flat)
assert disp_symbol.target_idx == 0
for int_result, symbol_result in zip(
disp_target_0.pd_results, disp_symbol.pd_results
):
assert_allclose(int_result.average, symbol_result.average)
assert_allclose(int_result["grid_values"], symbol_result["grid_values"])
# check that the pd plots are different for another target
disp_target_1 = PartialDependenceDisplay.from_estimator(
clf_int, iris.data, [0, 3], target=1, grid_resolution=grid_resolution
)
target_0_data_y = disp_target_0.lines_[0, 0].get_data()[1]
target_1_data_y = disp_target_1.lines_[0, 0].get_data()[1]
assert any(target_0_data_y != target_1_data_y)
multioutput_regression_data = make_regression(n_samples=50, n_targets=2, random_state=0)
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize("target", [0, 1])
def test_plot_partial_dependence_multioutput(pyplot, target):
# Test partial dependence plot function on multi-output input.
X, y = multioutput_regression_data
clf = LinearRegression().fit(X, y)
grid_resolution = 25
disp = PartialDependenceDisplay.from_estimator(
clf, X, [0, 1], target=target, grid_resolution=grid_resolution
)
fig = pyplot.gcf()
axs = fig.get_axes()
assert len(axs) == 3
assert disp.target_idx == target
assert disp.bounding_ax_ is not None
positions = [(0, 0), (0, 1)]
expected_label = ["Partial dependence", ""]
for i, pos in enumerate(positions):
ax = disp.axes_[pos]
assert ax.get_ylabel() == expected_label[i]
assert ax.get_xlabel() == f"x{i}"
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
def test_plot_partial_dependence_dataframe(pyplot, clf_diabetes, diabetes):
pd = pytest.importorskip("pandas")
df = pd.DataFrame(diabetes.data, columns=diabetes.feature_names)
grid_resolution = 25
PartialDependenceDisplay.from_estimator(
clf_diabetes,
df,
["bp", "s1"],
grid_resolution=grid_resolution,
feature_names=df.columns.tolist(),
)
dummy_classification_data = make_classification(random_state=0)
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize(
"data, params, err_msg",
[
(
multioutput_regression_data,
{"target": None, "features": [0]},
"target must be specified for multi-output",
),
(
multioutput_regression_data,
{"target": -1, "features": [0]},
r"target must be in \[0, n_tasks\]",
),
(
multioutput_regression_data,
{"target": 100, "features": [0]},
r"target must be in \[0, n_tasks\]",
),
(
dummy_classification_data,
{"features": ["foobar"], "feature_names": None},
"Feature 'foobar' not in feature_names",
),
(
dummy_classification_data,
{"features": ["foobar"], "feature_names": ["abcd", "def"]},
"Feature 'foobar' not in feature_names",
),
(
dummy_classification_data,
{"features": [(1, 2, 3)]},
"Each entry in features must be either an int, ",
),
(
dummy_classification_data,
{"features": [1, {}]},
"Each entry in features must be either an int, ",
),
(
dummy_classification_data,
{"features": [tuple()]},
"Each entry in features must be either an int, ",
),
(
dummy_classification_data,
{"features": [123], "feature_names": ["blahblah"]},
"All entries of features must be less than ",
),
(
dummy_classification_data,
{"features": [0, 1, 2], "feature_names": ["a", "b", "a"]},
"feature_names should not contain duplicates",
),
(
dummy_classification_data,
{"features": [1, 2], "kind": ["both"]},
"When `kind` is provided as a list of strings, it should contain",
),
(
dummy_classification_data,
{"features": [1], "subsample": -1},
"When an integer, subsample=-1 should be positive.",
),
(
dummy_classification_data,
{"features": [1], "subsample": 1.2},
r"When a floating-point, subsample=1.2 should be in the \(0, 1\) range",
),
(
dummy_classification_data,
{"features": [1, 2], "categorical_features": [1.0, 2.0]},
"Expected `categorical_features` to be an array-like of boolean,",
),
(
dummy_classification_data,
{"features": [(1, 2)], "categorical_features": [2]},
"Two-way partial dependence plots are not supported for pairs",
),
(
dummy_classification_data,
{"features": [1], "categorical_features": [1], "kind": "individual"},
"It is not possible to display individual effects",
),
],
)
def test_plot_partial_dependence_error(pyplot, data, params, err_msg):
X, y = data
estimator = LinearRegression().fit(X, y)
with pytest.raises(ValueError, match=err_msg):
PartialDependenceDisplay.from_estimator(estimator, X, **params)
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize(
"params, err_msg",
[
({"target": 4, "features": [0]}, "target not in est.classes_, got 4"),
({"target": None, "features": [0]}, "target must be specified for multi-class"),
(
{"target": 1, "features": [4.5]},
"Each entry in features must be either an int,",
),
],
)
def test_plot_partial_dependence_multiclass_error(pyplot, params, err_msg):
iris = load_iris()
clf = GradientBoostingClassifier(n_estimators=10, random_state=1)
clf.fit(iris.data, iris.target)
with pytest.raises(ValueError, match=err_msg):
PartialDependenceDisplay.from_estimator(clf, iris.data, **params)
def test_plot_partial_dependence_does_not_override_ylabel(
pyplot, clf_diabetes, diabetes
):
# Non-regression test to be sure to not override the ylabel if it has been
# See https://github.com/scikit-learn/scikit-learn/issues/15772
_, axes = pyplot.subplots(1, 2)
axes[0].set_ylabel("Hello world")
PartialDependenceDisplay.from_estimator(
clf_diabetes, diabetes.data, [0, 1], ax=axes
)
assert axes[0].get_ylabel() == "Hello world"
assert axes[1].get_ylabel() == "Partial dependence"
@pytest.mark.parametrize(
"categorical_features, array_type",
[
(["col_A", "col_C"], "dataframe"),
([0, 2], "array"),
([True, False, True], "array"),
],
)
def test_plot_partial_dependence_with_categorical(
pyplot, categorical_features, array_type
):
X = [[1, 1, "A"], [2, 0, "C"], [3, 2, "B"]]
column_name = ["col_A", "col_B", "col_C"]
X = _convert_container(X, array_type, columns_name=column_name)
y = np.array([1.2, 0.5, 0.45]).T
preprocessor = make_column_transformer((OneHotEncoder(), categorical_features))
model = make_pipeline(preprocessor, LinearRegression())
model.fit(X, y)
# single feature
disp = PartialDependenceDisplay.from_estimator(
model,
X,
features=["col_C"],
feature_names=column_name,
categorical_features=categorical_features,
)
assert disp.figure_ is pyplot.gcf()
assert disp.bars_.shape == (1, 1)
assert disp.bars_[0][0] is not None
assert disp.lines_.shape == (1, 1)
assert disp.lines_[0][0] is None
assert disp.contours_.shape == (1, 1)
assert disp.contours_[0][0] is None
assert disp.deciles_vlines_.shape == (1, 1)
assert disp.deciles_vlines_[0][0] is None
assert disp.deciles_hlines_.shape == (1, 1)
assert disp.deciles_hlines_[0][0] is None
assert disp.axes_[0, 0].get_legend() is None
# interaction between two features
disp = PartialDependenceDisplay.from_estimator(
model,
X,
features=[("col_A", "col_C")],
feature_names=column_name,
categorical_features=categorical_features,
)
assert disp.figure_ is pyplot.gcf()
assert disp.bars_.shape == (1, 1)
assert disp.bars_[0][0] is None
assert disp.lines_.shape == (1, 1)
assert disp.lines_[0][0] is None
assert disp.contours_.shape == (1, 1)
assert disp.contours_[0][0] is None
assert disp.deciles_vlines_.shape == (1, 1)
assert disp.deciles_vlines_[0][0] is None
assert disp.deciles_hlines_.shape == (1, 1)
assert disp.deciles_hlines_[0][0] is None
assert disp.axes_[0, 0].get_legend() is None
def test_plot_partial_dependence_legend(pyplot):
pd = pytest.importorskip("pandas")
X = pd.DataFrame(
{
"col_A": ["A", "B", "C"],
"col_B": [1, 0, 2],
"col_C": ["C", "B", "A"],
}
)
y = np.array([1.2, 0.5, 0.45]).T
categorical_features = ["col_A", "col_C"]
preprocessor = make_column_transformer((OneHotEncoder(), categorical_features))
model = make_pipeline(preprocessor, LinearRegression())
model.fit(X, y)
disp = PartialDependenceDisplay.from_estimator(
model,
X,
features=["col_B", "col_C"],
categorical_features=categorical_features,
kind=["both", "average"],
)
legend_text = disp.axes_[0, 0].get_legend().get_texts()
assert len(legend_text) == 1
assert legend_text[0].get_text() == "average"
assert disp.axes_[0, 1].get_legend() is None
@pytest.mark.parametrize(
"kind, expected_shape",
[("average", (1, 2)), ("individual", (1, 2, 20)), ("both", (1, 2, 21))],
)
def test_plot_partial_dependence_subsampling(
pyplot, clf_diabetes, diabetes, kind, expected_shape
):
# check that the subsampling is properly working
# non-regression test for:
# https://github.com/scikit-learn/scikit-learn/pull/18359
matplotlib = pytest.importorskip("matplotlib")
grid_resolution = 25
feature_names = diabetes.feature_names
disp1 = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
["age", "bmi"],
kind=kind,
grid_resolution=grid_resolution,
feature_names=feature_names,
subsample=20,
random_state=0,
)
assert disp1.lines_.shape == expected_shape
assert all(
[isinstance(line, matplotlib.lines.Line2D) for line in disp1.lines_.ravel()]
)
@pytest.mark.parametrize(
"kind, line_kw, label",
[
("individual", {}, None),
("individual", {"label": "xxx"}, None),
("average", {}, None),
("average", {"label": "xxx"}, "xxx"),
("both", {}, "average"),
("both", {"label": "xxx"}, "xxx"),
],
)
def test_partial_dependence_overwrite_labels(
pyplot,
clf_diabetes,
diabetes,
kind,
line_kw,
label,
):
"""Test that make sure that we can overwrite the label of the PDP plot"""
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 2],
grid_resolution=25,
feature_names=diabetes.feature_names,
kind=kind,
line_kw=line_kw,
)
for ax in disp.axes_.ravel():
if label is None:
assert ax.get_legend() is None
else:
legend_text = ax.get_legend().get_texts()
assert len(legend_text) == 1
assert legend_text[0].get_text() == label
@pytest.mark.parametrize(
"categorical_features, array_type",
[
(["col_A", "col_C"], "dataframe"),
([0, 2], "array"),
([True, False, True], "array"),
],
)
def test_grid_resolution_with_categorical(pyplot, categorical_features, array_type):
"""Check that we raise a ValueError when the grid_resolution is too small
respect to the number of categories in the categorical features targeted.
"""
X = [["A", 1, "A"], ["B", 0, "C"], ["C", 2, "B"]]
column_name = ["col_A", "col_B", "col_C"]
X = _convert_container(X, array_type, columns_name=column_name)
y = np.array([1.2, 0.5, 0.45]).T
preprocessor = make_column_transformer((OneHotEncoder(), categorical_features))
model = make_pipeline(preprocessor, LinearRegression())
model.fit(X, y)
err_msg = (
"resolution of the computed grid is less than the minimum number of categories"
)
with pytest.raises(ValueError, match=err_msg):
PartialDependenceDisplay.from_estimator(
model,
X,
features=["col_C"],
feature_names=column_name,
categorical_features=categorical_features,
grid_resolution=2,
)
@pytest.mark.parametrize("kind", ["individual", "average", "both"])
@pytest.mark.parametrize("centered", [True, False])
def test_partial_dependence_plot_limits_one_way(
pyplot, clf_diabetes, diabetes, kind, centered
):
"""Check that the PD limit on the plots are properly set on one-way plots."""
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
features=(0, 1),
kind=kind,
grid_resolution=25,
feature_names=diabetes.feature_names,
)
range_pd = np.array([-1, 1], dtype=np.float64)
for pd in disp.pd_results:
if "average" in pd:
pd["average"][...] = range_pd[1]
pd["average"][0, 0] = range_pd[0]
if "individual" in pd:
pd["individual"][...] = range_pd[1]
pd["individual"][0, 0, 0] = range_pd[0]
disp.plot(centered=centered)
# check that we anchor to zero x-axis when centering
y_lim = range_pd - range_pd[0] if centered else range_pd
padding = 0.05 * (y_lim[1] - y_lim[0])
y_lim[0] -= padding
y_lim[1] += padding
for ax in disp.axes_.ravel():
assert_allclose(ax.get_ylim(), y_lim)
@pytest.mark.parametrize("centered", [True, False])
def test_partial_dependence_plot_limits_two_way(
pyplot, clf_diabetes, diabetes, centered
):
"""Check that the PD limit on the plots are properly set on two-way plots."""
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
features=[(0, 1)],
kind="average",
grid_resolution=25,
feature_names=diabetes.feature_names,
)
range_pd = np.array([-1, 1], dtype=np.float64)
for pd in disp.pd_results:
pd["average"][...] = range_pd[1]
pd["average"][0, 0] = range_pd[0]
disp.plot(centered=centered)
contours = disp.contours_[0, 0]
levels = range_pd - range_pd[0] if centered else range_pd
padding = 0.05 * (levels[1] - levels[0])
levels[0] -= padding
levels[1] += padding
expect_levels = np.linspace(*levels, num=8)
assert_allclose(contours.levels, expect_levels)
def test_partial_dependence_kind_list(
pyplot,
clf_diabetes,
diabetes,
):
"""Check that we can provide a list of strings to kind parameter."""
matplotlib = pytest.importorskip("matplotlib")
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
features=[0, 2, (1, 2)],
grid_resolution=20,
kind=["both", "both", "average"],
)
for idx in [0, 1]:
assert all(
[
isinstance(line, matplotlib.lines.Line2D)
for line in disp.lines_[0, idx].ravel()
]
)
assert disp.contours_[0, idx] is None
assert disp.contours_[0, 2] is not None
assert all([line is None for line in disp.lines_[0, 2].ravel()])
@pytest.mark.parametrize(
"features, kind",
[
([0, 2, (1, 2)], "individual"),
([0, 2, (1, 2)], "both"),
([(0, 1), (0, 2), (1, 2)], "individual"),
([(0, 1), (0, 2), (1, 2)], "both"),
([0, 2, (1, 2)], ["individual", "individual", "individual"]),
([0, 2, (1, 2)], ["both", "both", "both"]),
],
)
def test_partial_dependence_kind_error(
pyplot,
clf_diabetes,
diabetes,
features,
kind,
):
"""Check that we raise an informative error when 2-way PD is requested
together with 1-way PD/ICE"""
warn_msg = (
"ICE plot cannot be rendered for 2-way feature interactions. 2-way "
"feature interactions mandates PD plots using the 'average' kind"
)
with pytest.raises(ValueError, match=warn_msg):
PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
features=features,
grid_resolution=20,
kind=kind,
)
@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
@pytest.mark.parametrize(
"line_kw, pd_line_kw, ice_lines_kw, expected_colors",
[
({"color": "r"}, {"color": "g"}, {"color": "b"}, ("g", "b")),
(None, {"color": "g"}, {"color": "b"}, ("g", "b")),
({"color": "r"}, None, {"color": "b"}, ("r", "b")),
({"color": "r"}, {"color": "g"}, None, ("g", "r")),
({"color": "r"}, None, None, ("r", "r")),
({"color": "r"}, {"linestyle": "--"}, {"linestyle": "-."}, ("r", "r")),
],
)
def test_plot_partial_dependence_lines_kw(
pyplot,
clf_diabetes,
diabetes,
line_kw,
pd_line_kw,
ice_lines_kw,
expected_colors,
):
"""Check that passing `pd_line_kw` and `ice_lines_kw` will act on the
specific lines in the plot.
"""
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 2],
grid_resolution=20,
feature_names=diabetes.feature_names,
n_cols=2,
kind="both",
line_kw=line_kw,
pd_line_kw=pd_line_kw,
ice_lines_kw=ice_lines_kw,
)
line = disp.lines_[0, 0, -1]
assert line.get_color() == expected_colors[0]
if pd_line_kw is not None and "linestyle" in pd_line_kw:
assert line.get_linestyle() == pd_line_kw["linestyle"]
else:
assert line.get_linestyle() == "--"
line = disp.lines_[0, 0, 0]
assert line.get_color() == expected_colors[1]
if ice_lines_kw is not None and "linestyle" in ice_lines_kw:
assert line.get_linestyle() == ice_lines_kw["linestyle"]
else:
assert line.get_linestyle() == "-"
def test_partial_dependence_display_wrong_len_kind(
pyplot,
clf_diabetes,
diabetes,
):
"""Check that we raise an error when `kind` is a list with a wrong length.
This case can only be triggered using the `PartialDependenceDisplay.from_estimator`
method.
"""
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
features=[0, 2],
grid_resolution=20,
kind="average", # len(kind) != len(features)
)
# alter `kind` to be a list with a length different from length of `features`
disp.kind = ["average"]
err_msg = (
r"When `kind` is provided as a list of strings, it should contain as many"
r" elements as `features`. `kind` contains 1 element\(s\) and `features`"
r" contains 2 element\(s\)."
)
with pytest.raises(ValueError, match=err_msg):
disp.plot()
@pytest.mark.parametrize(
"kind",
["individual", "both", "average", ["average", "both"], ["individual", "both"]],
)
def test_partial_dependence_display_kind_centered_interaction(
pyplot,
kind,
clf_diabetes,
diabetes,
):
"""Check that we properly center ICE and PD when passing kind as a string and as a
list."""
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 1],
kind=kind,
centered=True,
subsample=5,
)
assert all([ln._y[0] == 0.0 for ln in disp.lines_.ravel() if ln is not None])
def test_partial_dependence_display_with_constant_sample_weight(
pyplot,
clf_diabetes,
diabetes,
):
"""Check that the utilization of a constant sample weight maintains the
standard behavior.
"""
disp = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 1],
kind="average",
method="brute",
)
sample_weight = np.ones_like(diabetes.target)
disp_sw = PartialDependenceDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 1],
sample_weight=sample_weight,
kind="average",
method="brute",
)
assert np.array_equal(
disp.pd_results[0]["average"], disp_sw.pd_results[0]["average"]
)
def test_subclass_named_constructors_return_type_is_subclass(
pyplot, diabetes, clf_diabetes
):
"""Check that named constructors return the correct type when subclassed.
Non-regression test for:
https://github.com/scikit-learn/scikit-learn/pull/27675
"""
class SubclassOfDisplay(PartialDependenceDisplay):
pass
curve = SubclassOfDisplay.from_estimator(
clf_diabetes,
diabetes.data,
[0, 2, (0, 2)],
)
assert isinstance(curve, SubclassOfDisplay)
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